merge samples when combining m2 results

ylab-hi · Jul 9, 2024 · bd37722 · bd37722
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Prioritization of neoantigens is now done separately for each variant type (speeds up the process)
 - NMD information (e.g., escape rule,...) is now also calculated for all variants
 
+## [0.2.10] - 2024-07-08 
+
+### Fix 
+
+- Allow to combine multiple VCF files in indel detection using mutect2 (e.g., when multiple samples are provided)
+
 ## [0.2.9] - 2024-07-04
 
 ### Fix 

diff --git a/workflow/rules/indel.smk b/workflow/rules/indel.smk
@@ -347,7 +347,7 @@ rule combine_aug_short_indels_m2:
     "../envs/bcftools.yml"
   shell:
     """
-      bcftools concat --naive -O z {input} -o - | bcftools sort -O z -o {output} > {log} 2>&1
+      bcftools concat --naive-force -O z {input} -o - | bcftools sort -O z -o {output} > {log} 2>&1
     """
 
 rule select_SNVs_m2: